CHEMISTRY 1
STRUCTURES OF MOLECULES DISCUSSED IN CLASS

This page provides links to the structures of molecules discussed in class.
The structures come from a variety of sources which are indicated if known.
The coordinates of the structures are in the pdb (Brookhaven protein database) format which can be read by the viewer RasMol. Pomona students can
download the Berkeley version of RasMol from the directory v:\public\rasmol.

MOPAC is a package which solve the Schroedinger wave equation and calculates molecular orbitals of the valence electrons. The core electrons are handled empirically.

the crystal structure of the EDTA complex of manganese(II). Source: the Cambridge Structural Database System.

Crystal structures of binary ionic substances

The bond lengths are not drawn in several of these structures so to show the atoms in Rasmol, set the DISPLAY option to "space filling" or "balls and sticks". The structures have been downloaded from a Navy site and were converted from the xyz format to the pdb format. Rasmol can display structures in the xyz format but your browser must be set to recognize the MIME type (chemical) and subtype (x-xyz) and extension (xyz).

sodium chloride structure. The sodium cations fill all of the octahedral holes in a ccp lattice of chloride anions. The coordination number of each ion is 6.

zinc sulfide (sphalerite) structure. The zinc cations fill half of the tetrahedral holes in a ccp lattice of sulfide anions. The coordination number of each type of ion is 4.

fluorite structure. In the classic fluorite structure exhibited by the mineral fluorite, CaF2, the fluoride anions fill all of the tetrahedral holes in a ccp lattice of calcium ions. The case examined in class was Li2S which has the antifluorite structure in which the lithium cations fill all the tetrahedral holes in a ccp lattice of sulfide anions.